I found this interesting Single RNA-seq data set in GEO, but I am not sure how to analyze it appropriately.
They have deposited transcriptomic profiles of human and mouse pancreatic islets (pancreatic cells: Beta cells, Delta, etc). The problem I see is that the different pancreatic cell types are not in equal numbers: 872 Beta cells and 214 Delta cells.
I want to see whether the expression of a set of genes are correlated between the two cell types. I don't think that I can visualize the correlation between the expression of the Beta and Delta cells on a scatter plot if they are unequal in number. Is there a workaround to include all the cells in the analysis, without losing good quality transcriptome of beta/delta cell?
What I would like to do is to compare the expression of two pancreatic cell types (Beta v.s. Delta cells) using a scatter plot. I have a set of genes that I am interested in, and would like to see their expression profile for beta and delta cells. As far as I know, it is only possible to visualize this using a scatterplot (X:Beta vs Y:Delta) where the number of isolated beta cells is the same as the number of delta cells.
Question: Given unequal number of isolated panacriatic cells, what would be an appropriate way to compare the expression profiles? Should I just ignore the extra ones?
Any idea how to approch this problem?